R: Read SNV profile

read_profile {seqCAT}

R Documentation

Read SNV profile

Description

Read an SNV profile for use in downstream comparisons.

Usage

read_profile(file, sample_name, remove_mt = TRUE)

Arguments

`file`	The SNV profile to be read (path).
`sample_name`	The sample of the SNV profile (character).
`remove_mt`	Remove or keep mitochondrial variants (boolean).

Details

This is a function for reading SNV profiles created from VCF files. The data is returned as a GenomicRanges object, suitable for merging of metadata.

Value

A GRanges object.

Examples

# Path to test data
profile = system.file("extdata",
                      "test_1.profile.txt.gz",
                      package = "seqCAT")

# Read test profile
profile_1 <- read_profile(profile, "sample1")
profile_1 <- read_profile(profile, "sample1", remove_mt = FALSE)

[Package seqCAT version 1.4.1 Index]